Job ID = 9033302 sra ファイルのダウンロード中... Completed: 556935K bytes transferred in 7 seconds (585222K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 6903 0 6903 0 0 956 0 --:--:-- 0:00:07 --:--:-- 9932 100 27350 0 27350 0 0 3399 0 --:--:-- 0:00:08 --:--:-- 17934 100 64906 0 64906 0 0 7313 0 --:--:-- 0:00:08 --:--:-- 27584 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 26059381 spots for /home/okishinya/chipatlas/results/dm3/SRX969916/SRR1931632.sra Written 26059381 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:58 26059381 reads; of these: 26059381 (100.00%) were unpaired; of these: 1115069 (4.28%) aligned 0 times 19123330 (73.38%) aligned exactly 1 time 5820982 (22.34%) aligned >1 times 95.72% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4500362 / 24944312 = 0.1804 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 04 Jun 2017 00:27:46: # Command line: callpeak -t SRX969916.bam -f BAM -g dm -n SRX969916.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969916.20 # format = BAM # ChIP-seq file = ['SRX969916.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sun, 04 Jun 2017 00:27:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:27:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:27:46: # Command line: callpeak -t SRX969916.bam -f BAM -g dm -n SRX969916.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969916.10 # format = BAM # ChIP-seq file = ['SRX969916.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sun, 04 Jun 2017 00:27:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:27:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:27:46: # Command line: callpeak -t SRX969916.bam -f BAM -g dm -n SRX969916.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969916.05 # format = BAM # ChIP-seq file = ['SRX969916.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sun, 04 Jun 2017 00:27:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:27:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:27:51: 1000000 INFO @ Sun, 04 Jun 2017 00:27:52: 1000000 INFO @ Sun, 04 Jun 2017 00:27:52: 1000000 INFO @ Sun, 04 Jun 2017 00:27:56: 2000000 INFO @ Sun, 04 Jun 2017 00:27:57: 2000000 INFO @ Sun, 04 Jun 2017 00:27:57: 2000000 INFO @ Sun, 04 Jun 2017 00:28:02: 3000000 INFO @ Sun, 04 Jun 2017 00:28:02: 3000000 INFO @ Sun, 04 Jun 2017 00:28:03: 3000000 INFO @ Sun, 04 Jun 2017 00:28:07: 4000000 INFO @ Sun, 04 Jun 2017 00:28:07: 4000000 INFO @ Sun, 04 Jun 2017 00:28:08: 4000000 INFO @ Sun, 04 Jun 2017 00:28:12: 5000000 INFO @ Sun, 04 Jun 2017 00:28:12: 5000000 INFO @ Sun, 04 Jun 2017 00:28:14: 5000000 INFO @ Sun, 04 Jun 2017 00:28:17: 6000000 INFO @ Sun, 04 Jun 2017 00:28:17: 6000000 INFO @ Sun, 04 Jun 2017 00:28:19: 6000000 INFO @ Sun, 04 Jun 2017 00:28:22: 7000000 INFO @ Sun, 04 Jun 2017 00:28:23: 7000000 INFO @ Sun, 04 Jun 2017 00:28:24: 7000000 INFO @ Sun, 04 Jun 2017 00:28:27: 8000000 INFO @ Sun, 04 Jun 2017 00:28:28: 8000000 INFO @ Sun, 04 Jun 2017 00:28:30: 8000000 INFO @ Sun, 04 Jun 2017 00:28:32: 9000000 INFO @ Sun, 04 Jun 2017 00:28:33: 9000000 INFO @ Sun, 04 Jun 2017 00:28:35: 9000000 INFO @ Sun, 04 Jun 2017 00:28:38: 10000000 INFO @ Sun, 04 Jun 2017 00:28:38: 10000000 INFO @ Sun, 04 Jun 2017 00:28:40: 10000000 INFO @ Sun, 04 Jun 2017 00:28:43: 11000000 INFO @ Sun, 04 Jun 2017 00:28:43: 11000000 INFO @ Sun, 04 Jun 2017 00:28:46: 11000000 INFO @ Sun, 04 Jun 2017 00:28:47: 12000000 INFO @ Sun, 04 Jun 2017 00:28:49: 12000000 INFO @ Sun, 04 Jun 2017 00:28:51: 12000000 INFO @ Sun, 04 Jun 2017 00:28:52: 13000000 INFO @ Sun, 04 Jun 2017 00:28:54: 13000000 INFO @ Sun, 04 Jun 2017 00:28:56: 13000000 INFO @ Sun, 04 Jun 2017 00:28:57: 14000000 INFO @ Sun, 04 Jun 2017 00:29:00: 14000000 INFO @ Sun, 04 Jun 2017 00:29:02: 15000000 INFO @ Sun, 04 Jun 2017 00:29:02: 14000000 INFO @ Sun, 04 Jun 2017 00:29:05: 15000000 INFO @ Sun, 04 Jun 2017 00:29:07: 16000000 INFO @ Sun, 04 Jun 2017 00:29:07: 15000000 INFO @ Sun, 04 Jun 2017 00:29:11: 16000000 INFO @ Sun, 04 Jun 2017 00:29:11: 17000000 INFO @ Sun, 04 Jun 2017 00:29:13: 16000000 INFO @ Sun, 04 Jun 2017 00:29:16: 18000000 INFO @ Sun, 04 Jun 2017 00:29:16: 17000000 INFO @ Sun, 04 Jun 2017 00:29:18: 17000000 INFO @ Sun, 04 Jun 2017 00:29:21: 19000000 INFO @ Sun, 04 Jun 2017 00:29:22: 18000000 INFO @ Sun, 04 Jun 2017 00:29:24: 18000000 INFO @ Sun, 04 Jun 2017 00:29:26: 20000000 INFO @ Sun, 04 Jun 2017 00:29:28: 19000000 INFO @ Sun, 04 Jun 2017 00:29:29: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:29:29: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:29:29: #1 total tags in treatment: 20443950 INFO @ Sun, 04 Jun 2017 00:29:29: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:29:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:29:29: 19000000 INFO @ Sun, 04 Jun 2017 00:29:33: 20000000 INFO @ Sun, 04 Jun 2017 00:29:34: #1 tags after filtering in treatment: 20434332 INFO @ Sun, 04 Jun 2017 00:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:29:34: #1 finished! INFO @ Sun, 04 Jun 2017 00:29:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:29:35: 20000000 INFO @ Sun, 04 Jun 2017 00:29:36: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:29:36: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:29:36: #1 total tags in treatment: 20443950 INFO @ Sun, 04 Jun 2017 00:29:36: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:29:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:29:37: #2 number of paired peaks: 189 WARNING @ Sun, 04 Jun 2017 00:29:37: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:37: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:38: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:29:38: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:29:38: #1 total tags in treatment: 20443950 INFO @ Sun, 04 Jun 2017 00:29:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:29:40: #1 tags after filtering in treatment: 20434332 INFO @ Sun, 04 Jun 2017 00:29:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:29:40: #1 finished! INFO @ Sun, 04 Jun 2017 00:29:40: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:29:41: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:41: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:41: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:41: #2 predicted fragment length is 105 bps INFO @ Sun, 04 Jun 2017 00:29:41: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 04 Jun 2017 00:29:41: #2.2 Generate R script for model : SRX969916.20_model.r INFO @ Sun, 04 Jun 2017 00:29:41: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:29:41: #1 tags after filtering in treatment: 20434332 INFO @ Sun, 04 Jun 2017 00:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:29:41: #1 finished! INFO @ Sun, 04 Jun 2017 00:29:41: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:29:44: #2 number of paired peaks: 189 WARNING @ Sun, 04 Jun 2017 00:29:44: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:44: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:45: #2 number of paired peaks: 189 WARNING @ Sun, 04 Jun 2017 00:29:45: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:45: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:47: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:47: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:47: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:47: #2 predicted fragment length is 105 bps INFO @ Sun, 04 Jun 2017 00:29:47: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 04 Jun 2017 00:29:47: #2.2 Generate R script for model : SRX969916.05_model.r INFO @ Sun, 04 Jun 2017 00:29:47: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:29:48: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:48: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:48: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:48: #2 predicted fragment length is 105 bps INFO @ Sun, 04 Jun 2017 00:29:48: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 04 Jun 2017 00:29:48: #2.2 Generate R script for model : SRX969916.10_model.r INFO @ Sun, 04 Jun 2017 00:29:48: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:31:27: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:31:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:31:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:32:48: #4 Write output xls file... SRX969916.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:32:48: #4 Write peak in narrowPeak format file... SRX969916.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:32:48: #4 Write output xls file... SRX969916.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:32:48: #4 Write summits bed file... SRX969916.20_summits.bed INFO @ Sun, 04 Jun 2017 00:32:48: Done! INFO @ Sun, 04 Jun 2017 00:32:48: #4 Write peak in narrowPeak format file... SRX969916.05_peaks.narrowPeak pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2863 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:32:48: #4 Write summits bed file... SRX969916.05_summits.bed INFO @ Sun, 04 Jun 2017 00:32:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7665 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:32:52: #4 Write output xls file... SRX969916.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:32:52: #4 Write peak in narrowPeak format file... SRX969916.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:32:52: #4 Write summits bed file... SRX969916.10_summits.bed INFO @ Sun, 04 Jun 2017 00:32:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5138 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。